September 2026 - phenixbb - phenix-online.org

DEN restraints and ECHT disorder models
by Roberto Battistutta 20 Oct '26

20 Oct '26

Dear all, From which version of Phenix are the DEN restraints and ECHT disorder models implemented in the ensemble refinement (as described in Ploscariu, N., Burnley, T., Gros, P. & Pearce, N. M. (2021). Improving sampling of crystallographic disorder in ensemble refinement. Acta Cryst. D77, 1357-1364)? Thank you very much, Roberto. Roberto Battistutta Associate Professor Department of Chemical Sciences University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistutta(a)unipd.it

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emplace_local error funning from ChimeraX with 2.2-6143
by Kevin M Jude 30 Sep '26

30 Sep '26

Running Tools>Phenix>Local EM Fitting from ChimeraX 1.12, using phenix 2.2-6143, I get the failure pasted below. When I point ChimeraX to phenix 2.1-6048, the search is successful. phenix.voyager.emplace_local exited with error code 1 Command: /programs/i386-mac/phenix/2.2-6143/phenix_bin/phenix.voyager.emplace_local map1=half_map1.mrc map2=half_map2.mrc d_min=3.4 model_file=model.pdb sphere_center=(121.216,117.898,130.99) --json --json-filename emplace_local_result.json stdout: Starting phenix.voyager.emplace_local on Wed Sep 30 11:54:00 2026 by kjude =============================================================================== Processing files: ------------------------------------------------------------------------------- No files found Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- map1=half_map1.mrc map2=half_map2.mrc d_min=3.4 model_file=model.pdb sphere_center=(121.216,117.898,130.99) Final processed PHIL parameters: ------------------------------------------------------------------------------- model_file = model.pdb map1 = half_map1.mrc map2 = half_map2.mrc d_min = 3.4 sphere_center = (121.216,117.898,130.99) Starting job =============================================================================== Traceback (most recent call last): File "/opt/sbgrid/i386-mac/phenix/2.2-6143/lib/python3.11/site-packages/New_Voyager/scripts/em_placement_script.py", line 729, in em_placement_code results = prepare_docking_sphere( ^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/phenix/2.2-6143/lib/python3.11/site-packages/New_Voyager/_prepare_docking_sphere.py", line 55, in prepare_docking_sphere results = prepare_map_for_docking.assess_cryoem_errors( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/phenix/2.2-6143/lib/python3.11/site-packages/cctbx/maptbx/prepare_map_for_docking.py", line 1952, in assess_cryoem_errors total_ordered_volume = flex.mean(ordered_mm.map_data()) * unit_cell.volume() ^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'map_data' stderr: AttributeError: 'NoneType' object has no attribute 'map_data' During handling of the above exception, another exception occurred: Sorry: Search failed -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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Can Vidalista 80 Improve Relationship Confidence?
by danielbroown45＠gmail.com 30 Sep '26

30 Sep '26

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Recurring Payment: Making Regular Transactions Simple and Predictable
by wadekar.sagar087＠gmail.com 28 Sep '26

28 Sep '26

Recurring Payment is a financial arrangement that allows a customer to authorize a payment to be collected automatically at regular intervals. Instead of making the same payment manually each month, week, or year, the agreed amount can be processed according to a predefined schedule. This approach is commonly associated with subscriptions, memberships, utility bills, insurance premiums, loan repayments, and other ongoing services. One of the main characteristics of Recurring Payment is its scheduled nature. Once the payment arrangement is established, transactions can occur automatically on specified dates. Depending on the agreement, the amount may remain fixed or change according to usage, billing terms, or other conditions. Customers generally receive information about the payment schedule and applicable terms before the arrangement begins. Recurring payments can also influence how individuals and organizations manage their finances. For consumers, automatic transactions can reduce the need to remember multiple payment deadlines. For businesses, they can create a more structured billing process for services that continue over an extended period. However, users still need to monitor their accounts and review recurring transactions regularly to ensure that payments remain accurate and relevant. Security and transparency are important considerations. Payment providers may use authentication methods, transaction alerts, tokenization, and other safeguards to help protect payment information. Clear cancellation procedures are also important, particularly when a customer no longer needs a subscription or service. As digital commerce continues to develop, recurring payment arrangements are becoming a familiar part of everyday financial activity. Understanding the payment frequency, amount, renewal conditions, cancellation terms, and authorization requirements can help users make informed decisions about ongoing financial commitments. Read More @ https://www.marketresearchfuture.com/reports/recurring-payment-market-34776

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prediction.phenix-online.org maintenance
by Billy Poon 27 Sep '26

27 Sep '26

Hi all, The AlphaFold prediction server is currently undergoing some maintenance so predictions may fail intermittently. The server should be back to normal by Monday, September 28 around 9 am Pacific time. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 92R0129 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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Some about the phenix.real_space_refine with Cryo-EM refinement
by liulj＠ku.edu 08 Sep '26

08 Sep '26

Hello: I have a few questions/comments with phenix.real_space_refine on Cryo-EM structures that may need your clarification. I am running version 2.2-6143, but the previous 2.1-???? gave similar experience. Thanks! 1) ADP refinement seems to be seeded randomly among runs? With exactly same inputs, while the output coordinates (x,y,z) showed always to be exactly same, there are difference in B-factors. While most of those BFs showed marginal difference, some are actually not too small. For example: ATOM 19872 CG ASP D 609 160.261 175.386 111.504 1.00 94.06 C ATOM 19873 OD1 ASP D 609 159.374 176.102 110.995 1.00 98.69 O ATOM 19874 OD2 ASP D 609 161.312 175.850 111.994 1.00 97.73 O ---------------------------- ~30 A2 difference out of 60-90 A2 ---------- ATOM 19872 CG ASP D 609 160.261 175.386 111.504 1.00 66.78 C ATOM 19873 OD1 ASP D 609 159.374 176.102 110.995 1.00 71.45 O ATOM 19874 OD2 ASP D 609 161.312 175.850 111.994 1.00 64.91 O 2) I found also the default "rotamers.restraints.enabled=true" could really shift the rotamer's refinement adversely. It easily drops the favored rotamer percentage of a good model (refined or manually built) from above 90%s down to 70%s, and likely could never be refined back even with hard endeavors until it was turned off. This is very different experience from that in phenix.refine -- mostly it helped (at least do not set back largely if maps looked good) in the latter. 3) The "rotamers.fit=outliers_or_poormap", upon my tests, is another interesting default? The "outliers_and_poormap" option mostly worked much better for me, while the former one can shift large regional chains a lot (like push long chain out of map; sounds like much over weighted for their contribution?). This even drove me think if there exists a confusion between Boolean and natural languages for this default? 4) Does the default "weight=None" mean this was turned off/NA currently, and all weights were set automatically.... I tested with different values but did not make changes (but BFs as mentioned in 1) above). The instruction says it could be invoked... Best regards, Lijun

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Mac installation problem
by Engin Özkan 06 Sep '26

06 Sep '26

Hi, When I try to install the latest release (2.2.1) on an M1 MacBook Pro using the GUI installer, I get the error "The operation couldn’t be completed. (com.apple.installer.pagecontroller error -1.) Couldn't open "Phenix-2.2.1-6174-MacOSX-arm64.pkg" I have already removed extended attributes, so that's not the problem. Checking xattr gives this % xattr ~/Downloads/Phenix-2.2.1-6174-MacOSX-arm64.pkg com.apple.macl This is also not a time-out issue; the installer just never launches. Best, Engin -- Engin Özkan, Ph.D. Associate Professor Dept of Biochemistry and Molecular Biology University of Chicago http://ozkan.uchicago.edu

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